GdBaCo2O5.5 exhibits impressive application potentials on giant magnetic resistance materials and solid oxide fuel cell cathodes, owing to its unique electrical and magnetic properties. In this article, stable magnetic-order structures of Co in GdBaCo2O5.5, Fe doped compounds, and GdBaCo2O5.25 with additional oxygen vacancy deficients, are investigated based on first principles calculations. Comparisons with reported experiments are also presented. It turns out that G type antiferromagnetic ordering is the most stable under ground state, and Co is high-spin state, which matches the observations of neutron diffraction and XAS spectrum. Calculated results show that the stability of ferromagnetic phase under low temperature will be enhanced by the introduction of Fe dopant, which is supported by the reported experiment. Moreover, additional oxygen vacancies caused by the valence alternation of Co ions are discussed. The magnetic moments of several Co cations closed to the additional vacancy are reduced. Besides, oxygen ions could be divided into 3 layers based on their stabilities. Oxygen vacancy formation energies within two layers are much lower, which facilitate the oxygen ion transfer along these layers. This result also fits the conclusion of reported molecular dynamic simulation well. (C) 2016 Elsevier B.V. All rights reserved.